The peakml viewer
The peakml viewer can be found in the files menu hidden
in one of the folders or you can install/run it directly from the R by using PeakML.Viewer () command from mzmatch.R package.
A user interface application called PeakML Viewer enables quick visualisation, inspection and manipulation of the contents
of a PeakML file (e.g. manual selection and/or export of peaks of interest).
After loading a PeakML file, the ``entry'' view gives an overview of all the entries with the retention time, mass and intensity.
The ordering from the original file is kept intact, making the results from sorting tools like
accessible. An entry is highlighted in bold when it has been matched to a compound from a database with
(determined by verifying whether the entry contains the system-defined annotation identification). By clicking on an entry, the
associated traces will be displayed in the "graph" view and the identifications in the "identification" view (including
the ppm-deviation and the putatively assigned molecular structure when available). There is an additional tab derivatives,
which shows all the clustered related peaks with their identification as determined by
(stored in the system defined annotations relation.id and relation.ship). The "filter" view allows the user to perform
simple operations on the data (sorting and filtering), for zooming in on the entries of interest. The "trend" view gives an
overview of the intensity levels for each entry (which in the case of a peakset can for example consist of multiple
mass chromatograms). All the peaks belonging to the same set are grouped together in this plot and the mean, minimum and
maximum values are displayed. The "sets" view shows all the measurements used and how they are organized in sets. With
the check boxes all the peaks from a set or peaks individually can be switched on or off (i.e. not displayed). The
"annotations" view gives an overview of all the annotations that are available for the current entry.